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| author | Frederick Muriuki Muriithi | 2021-10-19 09:16:38 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2021-10-19 09:16:38 +0300 |
| commit | 3304fa682924b8f6bff5126ecf2fb58f4201b968 (patch) | |
| tree | 7f9d097e0234b086533c2eb36c9d57e59d267949 /tests/unit | |
| parent | c5355c5db72fdec9e7e360ceec19d5d50d15ce00 (diff) | |
| download | genenetwork3-3304fa682924b8f6bff5126ecf2fb58f4201b968.tar.gz | |
Implement `dictify_by_samples`
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: implement `dictify_by_samples` function
* tests/unit/test_partial_correlations.py: implement tests for
`dictify_by_samples` function
Implement the `dictify_by_samples` function as a partial migration of the
`web.webqtl.correlation.correlationFunction.fixStrains` function from GN1.
Diffstat (limited to 'tests/unit')
| -rw-r--r-- | tests/unit/test_partial_correlations.py | 42 |
1 files changed, 41 insertions, 1 deletions
diff --git a/tests/unit/test_partial_correlations.py b/tests/unit/test_partial_correlations.py index 0083ef7..6302f74 100644 --- a/tests/unit/test_partial_correlations.py +++ b/tests/unit/test_partial_correlations.py @@ -1,7 +1,7 @@ """Module contains tests for gn3.partial_correlations""" from unittest import TestCase -from gn3.partial_correlations import control_samples +from gn3.partial_correlations import control_samples, dictify_by_samples sampleslist = ["B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"] control_traits = ( @@ -85,3 +85,43 @@ class TestPartialCorrelations(TestCase): ((None, None, None, None, None, None), (None, None, None, None), (None, None, None)), (6, 4, 3))) + + def test_dictify_by_samples(self): + """ + Given: + a sequence of sequences with sample names, values and variances, as + in the output of `gn3.partial_correlations.control_samples` or + the output of `gn3.db.traits.export_informative` + When: + the sequence is passed as an argument into the + `gn3.partial_correlations.dictify_by_sample` + Then: + return a sequence of dicts with keys being the values of the sample + names, and each of who's values being sub-dicts with the keys + 'sample_name', 'value' and 'variance' whose values correspond to the + values passed in. + """ + self.assertEqual( + dictify_by_samples( + ((("B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"), + ("BXD12", "BXD16", "BXD19", "BXD2"), + ("B6cC3-1", "BXD1", "BXD2")), + ((7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944), + (8.39265, 8.17443, 8.30401, 7.80944), + (7.51879, 7.77141, 7.80944)), + ((None, None, None, None, None, None), (None, None, None, None), + (None, None, None)), + (6, 4, 3))), + ({"B6cC3-1": {"sample_name": "B6cC3-1", "value": 7.51879, "variance": None}, + "BXD1": {"sample_name": "BXD1", "value": 7.77141, "variance": None}, + "BXD12": {"sample_name": "BXD12", "value": 8.39265, "variance": None}, + "BXD16": {"sample_name": "BXD16", "value": 8.17443, "variance": None}, + "BXD19": {"sample_name": "BXD19", "value": 8.30401, "variance": None}, + "BXD2": {"sample_name": "BXD2", "value": 7.80944, "variance": None}}, + {"BXD12": {"sample_name": "BXD12", "value": 8.39265, "variance": None}, + "BXD16": {"sample_name": "BXD16", "value": 8.17443, "variance": None}, + "BXD19": {"sample_name": "BXD19", "value": 8.30401, "variance": None}, + "BXD2": {"sample_name": "BXD2", "value": 7.80944, "variance": None}}, + {"B6cC3-1": {"sample_name": "B6cC3-1", "value": 7.51879, "variance": None}, + "BXD1": {"sample_name": "BXD1", "value": 7.77141, "variance": None}, + "BXD2": {"sample_name": "BXD2", "value": 7.80944, "variance": None}})) |